Human evolution tied to a small fraction of the genome – “Only about 7.5 percent of the human genetic instruction book shaped the evolution of human traits, a new study suggests. And it’s often not genes, but the how-to instructions for using those genes that are most important, researchers report January 19 in Nature Genetics…. Previously, researchers have mostly looked for evolutionary clues in protein-producing genes because proteins do much of the important work in cells and organisms. Altering a protein may change the way an organism looks or acts. But mutations that alter proteins often are devastating to an organism and therefore aren’t passed on to offspring. Gulko and colleagues found that only 9 percent of the DNA that got evolution’s attention resides in protein-coding parts of the genome that are shared with other species. About 52 percent of the places showing signs of natural selection were in intergenic regions, the stretches of DNA between genes. Another 35 percent were in introns — spacer DNA found within genes but not involved in encoding proteins. Both intergenic regions and introns often contain DNA responsible for controlling gene activity. These findings suggest that human evolution works mostly through changes in how genes are used, rather than by altering genes and the proteins they encode.”

Kennewick Man was Native American – “‘Genetic analysis is still under way in Denmark, but documents obtained through the federal Freedom of Information Act say preliminary results point to a Native-American heritage.'” – from dienekes. see also from razib: Native Americans Are Evolutionarily Elegant – “One insight of modern ancient DNA is that there has been a great deal of population turnover over the past ~10,000 years, as well as admixture between disparate lineages. When Kennewick Man died ~9,000 years ago Europeans as we understand them did not exist genetically.”

The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States – “Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.” – see also: The Fluidity of Race from greg cochran.

Largest-ever autism genome study finds most siblings have different autism-risk genes – “In the new study, Dr. Scherer’s team sequenced 340 whole genomes from 85 families, each with two children affected by autism. The majority of siblings (69 percent) had little to no overlap in the gene variations known to contribute to autism. They found that the sibling pairs shared the same autism-associated gene changes less than one third of the time (31 percent). The findings challenge long-held presumptions. Because autism often runs in families, experts had assumed that siblings with the disorder were inheriting the same autism-predisposing genes from their parents. It now appears this may not be true.” – h/t shrikant mantri!

Genetic mutation for metabolic disease identified within an Inuit population – “The disease in question, glycogen storage disease type IIIa, is caused by mutations in the AGL gene, leading to less-active glycogen-debranching enzymes. The disorder disrupts the body’s capacity to release sugar from glycogen, resulting in the formation of damaging glycogen deposits…. Glycogen storage disease IIIa affects around one in 100,000 people in North America. However, the researchers estimate that the disorder may affect around 1 in 2,500 people in Nunavik – the homeland of the Inuit in Quebec.” – maybe they should stick to eating seal blubber. srsly!

Admixture in the Americas: Admixture among US Blacks and Hispanics and academic achievement – “[W]e see the expected directions and order, for Blacks (who are mostly African), American admixture is positive and European is more positive…. We do not see the expected results per genetic model. Among Hispanics who are 73% European, African admixture has a positive relationship to academic achievement. American admixture is negatively correlated and European positively, but weaker than African. The only thing that’s in line with the genetic model is that European is positive. On the other hand, results are not in line with a null model either….” – from emil kirkegaard.

School – “In summary, it very much looks like more years of education are associated with an increase in intelligence test scores, but not anything like as strongly to underlying general intelligence or to underlying basic processing speeds.” – from dr. james thompson.

Genetic Pleiotropy Explains Associations between Musical Auditory Discrimination and Intelligence – “[A] large sample of Swedish twins (N = 10,500) was used to investigate the genetic architecture of the associations between intelligence and performance on three musical auditory discrimination tasks (rhythm, melody and pitch). Phenotypic correlations between the tasks ranged between 0.23 and 0.42 (Pearson r values). Genetic modelling showed that the covariation between the variables could be explained by shared genetic influences. Neither shared, nor non-shared environment had a significant effect on the associations. Good fit was obtained with a two-factor model where one underlying shared genetic factor explained all the covariation between the musical discrimination tasks and IQ, and a second genetic factor explained variance exclusively shared among the discrimination tasks. The results suggest that positive correlations among musical aptitudes result from both genes with broad effects on cognition, and genes with potentially more specific influences on auditory functions.” – h/t rosalind arden!

The Role of Parenting in the Prediction of Criminal Involvement: Findings From a Nationally Representative Sample of Youth and a Sample of Adopted Youth [pdf] – “The role of parenting in the development of criminal behavior has been the source of a vast amount of research, with the majority of studies detecting statistically significant associations between dimensions of parenting and measures of criminal involvement. An emerging group of scholars, however, has drawn attention to the methodological limitations — mainly genetic confounding — of the parental socialization literature. The current study addressed this limitation by analyzing a sample of adoptees to assess the association between 8 parenting measures and 4 criminal justice outcome measures. The results revealed very little evidence of parental socialization effects on criminal behavior before controlling for genetic confounding and no evidence of parental socialization effects on criminal involvement after controlling for genetic confounding.” – h/t jayman!

Hospitals Aim to Better Match Blood Donors and Recipients – “People fall into one of four main blood groups — A, B, AB and O — and they have a so-called Rh factor that is either positive or negative. But scientists over the last few decades have discovered around 33 blood groups and continue to identify more. Each group also contains multiple variations that go to make up a patient’s exact blood type.”

Ageing research: Blood to blood – “By splicing animals together, scientists have shown that young blood rejuvenates old tissues. Now, they are testing whether it works for humans.” – parabiosis. it’s baaaack!

Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa [pdf] – “Here we analyze the saliva microbiome from native Alaskans (76 individuals from 4 populations), Germans (10 individuals from 1 population), and Africans (66 individuals from 3 populations) based on next-generation sequencing of partial 16S rRNA gene sequences. After quality filtering, a total of 67,916 analyzed sequences resulted in 5,592 OTUs (defined at ≥97% identity) and 123 genera. The three human groups differed significantly by the degree of diversity between and within individuals (e.g. beta diversity: Africans > Alaskans > Germans; alpha diversity: Germans > Alaskans > Africans). UniFrac, network, ANOSIM, and correlation analyses all indicated more similarities in the saliva microbiome of native Alaskans and Germans than between either group and Africans. The native Alaskans and Germans also had the highest number of shared bacterial interactions.”

Tuberculosis genomes track human history – “A study of nearly 5,000 samples of Mycobacterium tuberculosis from around the world shows how a lineage of the bacterium that emerged thousands of years ago in Asia has since become a global killer that is widely resistant to antibiotic drugs. Although M. tuberculosis probably first emerged some 40,000 years ago in Africa, the disease did not take hold until humans took to farming…. [T]he common ancestor of all the M. bacterium strains circulating today began spreading around 10,000 years ago in the ancient Fertile Crescent, a region stretching from Mesopotamia to the Nile Delta that was a cradle of agriculture…. But of all the M. bacterium strains circulating today, few strike more fear in public-health officials than the ‘Beijing lineage’. First identified in greater Beijing in the mid-1990s, this lineage now circulates throughout the world and many strains are resistant to drugs that vanquish other types of TB…. Consistent with its name, the Beijing lineage did indeed emerge near north-eastern China…. And it did so around 6,600 years ago, the researchers found, which coincides with archaeological evidence for the beginnings of rice farming in China’s upper Yangtze River valley.” – h/t billare!

Your Friends Know How Long You Will Live: A 75-Year Study of Peer-Rated Personality Traits – “To test whether friends’ reports of personality predict mortality risk, we used data from a 75-year longitudinal study (the Kelly/Connolly Longitudinal Study on Personality and Aging). In that study, 600 participants were observed beginning in 1935 through 1938, when they were in their mid-20s, and continuing through 2013. Male participants seen by their friends as more conscientious and open lived longer, whereas friend-rated emotional stability and agreeableness were protective for women. Friends’ ratings were better predictors of longevity than were self-reports of personality, in part because friends’ ratings could be aggregated to provide a more reliable assessment.”

Voluntary Activities and Daily Happiness in the US [pdf] – “This paper analyzes differences in daily happiness between those individuals in the United States who perform voluntary activities during the day, and those who do not…. [T]hose who devote any time to voluntary activities during the day report higher levels of daily happiness than those who do not…. [W]hen the issue of reverse causality is taken into account, we find no differences in daily happiness between volunteers and non-volunteers, which indicates that happier individuals are also more likely to volunteer.” – h/t ben southwood!

Aberrant Gene Expression in Humans – “The uniqueness of individuals is due to differences in the combination of genetic, epigenetic and environmental determinants. Understanding the genetic basis of phenotypic variation is a key objective in genetics…. One of our major findings is that private SNPs may contribute to aberrant expression in outlier individuals. These private SNPs are more frequently located in the enhancer and promoter regions of genes that are aberrantly expressed, suggesting a possible regulatory function of these SNPs.”

Recurrent loss of sex is associated with accumulation of deleterious mutations in Oenothera – “Sexual reproduction is nearly universal among eukaryotes. Theory predicts that the rarity of asexual eukaryotic species is in part caused by accumulation of deleterious mutations and heightened extinction risk associated with suppressed recombination and segregation in asexual species. We tested this prediction with a large dataset of 62 transcriptomes from 29 species in the plant genus Oenothera, spanning 10 independent transitions between sexual and a functionally asexual genetic system called permanent translocation heterozygosity…. These results confirm that an important advantage of sex is that it facilitates selection against deleterious alleles, which might help to explain the dearth of extant asexual species.” – h/t melissa wilson sayres!

Lewontin wins the Crafoord Prize – “The Crafoord Prize for 2015 was awarded to Richard Lewontin and Tomoko Ohta, for their discovery that there was very much more genetic variation that had been expected. Lewontin discovered this using protein gel electrophoresis to study a number of loci in Drosophila. It’s an important result. The problem is, virtually everything he’s said and done since that time has been a pile of steaming ideological crap.” – from greg cochran.

Single Markers Tell You Only a Bit About Individual Ancestry – “A new paper in The American Journal of Human Genetics, Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup, tells you something which should be obvious: one marker tells you only so much about individual ancestry. In other words, the history of one gene can only tell you so much about the whole genome. Because mtDNA and Y chromosome* does not recombine you can treat it as one long genetic marker…. But Richard Lewontin’s insight that a great deal of human genetic variation is not partitioned across populations, but within them, applies to mtDNA and the Y chromosomes as well. Where Lewontin’s insight misleads is that using just a few more markers one can obtain relatively robust phylogenetic trees which reflect well the population structure and history of a given species.” – also from razib.

The Economist takes a half step forwards – “They do not examine the usual finding that educated parents are more influential than rich parents in supposedly ‘boosting’ intelligence. They leave out the genetic element entirely, and say it is ‘incomes’ which are inherited. If so adoption into a rich household should have massive effects on intellect, but that is not found. If adoption cannot wipe the slate clean, what chance a kindergarten?” – from dr. james thompson.

Gender divide in religious belief, survey suggests – “A big gender divide exists between men and women in their 40s in belief in God and life after death, a poll suggests. Of the British men surveyed, 54% said they were atheists or agnostics compared with only 34% of women. The study also showed that Muslims in the survey had the fewest doubts about the existence of God and the afterlife. The research involving more than 9,000 British people born in 1970 was analysed at the University of Essex.” – h/t ed west! who tweeted: “71% of evangelical Christians have no doubts about God’s existence. 33% of Catholics, 16% of Anglicans & Methodists.”

Thumb bones in pre-humans make them more like us, study says – “Some of our tree-swinging pre-human ancestors may have been a bit more like us than previously thought, thanks to a tiny section of their thumbs. One key attribute that separates humans from other animals is our opposable thumb, and the way parts of the thumb are structured to allow for a strong yet precise grip that fostered advanced use of tools. It’s what allows us to throw items more precisely, pick guitars and turn a key. And now, thanks to high-tech tools of our own, scientists have determined that a couple million years ago one of our pre-human ancestors had the same human-defining precision grip, even though researchers think of them as little more than upright walking apes, according to a study published Thursday in the journal Science. That supports earlier but controversial evidence that the small-brained Australopithecus africanus fashioned early tools.” – h/t regular ron!

Thomas Cromwell was the Islamic State of his day – “No one can be sure of the exact figure, but it is estimated that the destruction started and legalised by Cromwell amounted to 97% of the English art then in existence. Statues were hacked down. Frescoes were smashed to bits. Mosaics were pulverized. Illuminated manuscripts were shredded. Wooden carvings were burned. Precious metalwork was melted down. Shrines were reduced to rubble.”

bonus bonus bonus bonus bonus: All in the (bigger) family – “A decade of genetic data and other evidence has persuaded most researchers that insects and crustaceans, long considered widely separated branches of the arthropod family, actually belong together. The new arthropod tree puts hexapods — six-limbed creatures that include insects, springtails, and silverfish — as closer kin to crabs, lobster, shrimp, and crayfish than those ‘standard’ crustaceans are to others such as seed shrimp.”

New data reveal extent of genetic overlap between major mental disorders – gwas study**: “[T]he overlap was highest between schizophrenia and bipolar disorder; moderate for bipolar disorder and depression and for ADHD and depression; and low between schizophrenia and autism. Overall, common genetic variation accounted for 17-28 percent of risk for the illnesses.” (**that’s redundant, isn’t it? sorry.)

Common genes may underlie alcohol dependence, eating disorders – “In a study of nearly 6,000 adult twins, researchers found that common genetic factors seemed to underlie both alcoholism and certain eating disorder symptoms—namely, binge eating and purging habits, such as self-induced vomiting or laxative abuse. Genes appeared to explain 38 percent to 53 percent of the risk of developing those disorders.”

African genes tracked back – “[The researchers] saw signs reflecting two waves of migration: one about 3,000 years ago, of non-Africans entering east Africa, and a second one 900–1,800 years ago, as east Africans migrated to southern Africa and brought non-African genes along with them…. Because of this two-step migration, some Khoe-San groups who were thought to have been genetically quite isolated actually carry 1–5% non-African DNA….”

Handaxe design reveals distinct Neanderthal cultures – “Two cultural traditions existed among Neanderthals living in what is now northern Europe between 115,000 to 35,000 years ago…. [T]wo separate handaxe traditions or designs existed – one in a region now spanning south-western France and Britain – the other in Germany and further to the East.”

The Behavioral Ecology of Chimpanzee War and Liberal Peace – “[V]iolent aggression among humans and chimps is a flexible natural propensity that tends to be stronger in males than in females, and the expression of that propensity depends on the social circumstances that determine the relative costs and benefits of violent fighting.” – @darwinian conservatism.

There is no hope of democracy in the Middle East – “Most people, in other times and other places, have lived in societies more like Game of Thrones than Borgen, clannish rather than democratic, where people feel their loyalty and duty is towards other members of their extended family or religious community. To get people to work in the best interests of strangers so that you accept their authority when they get more people into the polling booth than you, is an achievement, not a natural state…. Egypt is an ancient civilisation but it is a clannish society….” – from ed west. (^_^) see also: Ed West interview: debating the ‘illusions’ of a diverse society.

Steven Pinker, Science, and “Scientism” – “In reality, the issue here is not whether this imaginary ‘science’ object exists and, assuming it does, whether it is ‘good’ or ‘evil.’ It is about whether we should be empowered to learn things about the universe in which we live or not. The opponents of ‘scientism’ typically rail against such things as eugenics, Social Darwinism, and the atomic bomb. These are supposedly the creations of the ‘science’ object. But, in fact, they are no such thing.” – really good stuff @helian unbound. via hbd bibliography. also from h.u. (he’s on a roll this week): Of Ingroups, Outgroups and Ideology.

How the light gets out – re. consciousness: “…the attention schema theory. It says that awareness is not something magical that emerges from the functioning of the brain. When you look at the colour blue, for example, your brain doesn’t generate a subjective experience of blue. Instead, it acts as a computational device. It computes a description, then attributes an experience of blue to itself. The process is all descriptions and conclusions and computations. Subjective experience, in the theory, is something like a myth that the brain tells itself. The brain *insists* that it has subjective experience because, when it accesses its inner data, it finds that information.”

Notes from Beijing: About That Chinese Social Contract – “The traditional Chinese social contract was not a compact between individuals and the state, but a compact between Chinese society as a whole and the state…. Self interested calculations of rational individuals coolly weighing their economic and political interests never really seemed to be part of the program.” – from t. greer.

Genomic Differences Found in Types of Cervical Cancer – “…the spectrum of cancer-related gene mutations in the two main subtypes of cervical cancer — adenocarcinoma and squamous cell carcinoma. In tests on 80 cervical tumor samples, the investigators found high rates of mutations in two genes: PIK3CA and KRAS. While PIK3CA mutations appeared in both subtypes, KRAS mutations were found only in adenocarcinomas.”

US behavioural research studies skew positive – “US behavioural researchers have been handed a dubious distinction — they are more likely than their colleagues in other parts of the world to exaggerate findings, according to a study published today.”

bonus: Birds know road speed limits – “Crows, house sparrows and other species judge when to flee the asphalt by average traffic rates rather than an oncoming car’s speed.”

bonus bonus: Beetles eat greedy offspring Edinburgh University research finds – “Burying beetles occasionally punish young who nag for food by eating those who pester them most…. It encourages the larvae to plead more honestly according to how hungry they are and not try to outdo their siblings by pestering their mother for food.” – so there!

bonus bonus bonus: Saudi Arabia’s War on Witchcraft – “A special unit of the religious police pursues magical crime aggressively, and the convicted face death sentences.”

not sure if this is a late linkfest from this past sunday or an early linkfest for next sunday…. (~_^)

Patterns of selection on Neanderthal alleles in modern humans – “‘We identified Neandertal alleles that are at higher frequency than expected under a model of neutral evolution, and identify dozens of genomic locations in Europeans and East Asians at which the Neandertal alleles are the targets of positive selection. Interestingly, there is evidence for more extensive positive selection in East Asian than in European populations.'” – @race/history/evolution notes.

Paternal age and fitness in pre-industrial Finland – “‘Individuals whose fathers, grandfathers and great-grandfathers fathered their lineage at age of 20 were ~9% more likely to survive to adulthood than those with 40-year-old male ancestors.'” – @race/history/evolution notes.

Law alone? – “People of northwestern European descent put the least emphasis on the blood bond of a nation’s population…. The paradox presented here for many like myself is that the places inspiring the warmest feelings and that I would like most to live in are the places that tend to put the least effort into maintaining what they have. It’s tragic.” – yup. =/ from the awesome epigone.

Ethnic background influences immune response to TB – “Over the thousands of years that humans have been infected with TB, people of different ethnicities have evolved different immune mechanisms for handling the bacteria, a finding that could affect the outcome of planned trials for new TB drugs…. [D]ifferences in the way TB affects the body are also linked to ethnicity. For example, he found that most infections in Europeans are in the lungs, for example, while Asians and Africans get most TB infections in other organs.” – @new scientist. also: Scientists discover ethnic differences in immune response to TB bacterium.

Chinese People May Be at Higher Risk for Stroke Than Caucasians – “[T]he research found a slightly higher overall risk of stroke in Chinese people than in Caucasians, with a range of 205 to 584 strokes per 100,000 Chinese people age 45 to 74, compared to 170 to 335 strokes per 100,000 Caucasian people the same age. Chinese also had a higher risk of intracerebral hemorrhage, a type of stroke due to bleeding into the brain from a ruptured blood vessel, compared to Caucasian people, or 33 percent of all strokes compared to 12 percent of all strokes in community-based studies. Chinese people had a lower average age of stroke onset of 66 to 70 years-old, compared to 72 to 76 years-old for Caucasians.” – via hbd bibliography!

Poles in the Tent – “[I]f high-quality protein were the long pole in the tent, male provisioning of meat, which we see in chimpanzees, might matter quite a bit more than you would think from the number of calories alone.” – from greg cochran.

Dark Counsel From The Durants – “‘Inequality is not only natural and inborn, it grows with the complexity of civilization. Hereditary inequalities breed social and artificial inequalities; every invention or discovery is made or seized by the exceptional individual, and makes the strong stronger, the weak relatively weaker, than before.'” – dark stuff, indeed! from malcolm pollack. here’s the durants’ The Lessons of History.

bonus bonus bonus bonus bonus bonus bonus: Isolated Afghans contemplate mass exodus – “The 1,100 ethnic Kyrgyz living in this isolated sliver of Afghanistan wedged between Tajikistan, Pakistan and China have been spared the violence that has plagued the rest of their country. But they have also done without the burst of foreign aid that has helped reconstruct one of the world’s poorest nations.”

bonus bonus bonus bonus bonus bonus bonus bonus: A Village Invents a Language All Its Own – “The language, called Warlpiri rampaku, or Light Warlpiri, is spoken only by people under 35 in Lajamanu, an isolated village of about 700 people in Australia’s Northern Territory. In all, about 350 people speak the language as their native tongue.”

The Strange Case of Dr. Robert Trivers – “[Trivers] has been driven off the campus of Rutgers University! He has been involved in a controversy lately over his accusation that one of his graduate students committed fraud in a scientific paper. Apparently he was banned from campus because a colleague who supports the alleged fraudster claimed Trivers had ‘frightened him in his office’.” – from helian unbound.

The Pattern of Female Nuptiality in Oman – “[M]ore than half (52%) of the total marriages in Oman are consanguineous. First cousin unions are the most common type of consanguineous unions, constituting 39% of all marriages and 75% of all consanguineous marriages. About 11% of the marriages are polygynous…. [P]aternal first-cousin marriages constituted 27.7% of all marriages and 72% (565/786) of all first-cousin marriages, while maternal first-cousin marriages constituted 10.8% of all marriages and 28% (221/786) of all first-cousin marriages.”

Could Life Be Older Than Earth Itself? – “[T]wo geneticists have applied Moore’s Law to the rate at which life on Earth grows in complexity — and the results suggest organic life first came into existence long before Earth itself.”